SMTL ID : 4ivq.1

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with IN43/5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x I43: 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-4-methoxy-1,5-dimethylpyrimidin-2(1H)-one(Non-covalent)

I43.1: 11 residues within 4Å: Chain A: H.13, E.38, W.43, I.52, Y.56, Q.80, M.83, R.118, Y.127, R.131, M.186 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.127 Hydrogen bonds: A:K.17, A:K.17, A:E.38, A:R.118, A:R.131 pi-Stacking: A:Y.127 I43.4: 14 residues within 4Å: Chain B: H.13, E.38, W.43, I.52, I.55, Y.56, Q.80, M.83, R.118, A.123, Y.127, R.131, R.177, M.186 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.127 Hydrogen bonds: B:E.38, B:R.118 Water bridges: B:R.131, B:R.131 pi-Stacking: B:Y.127

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: H.13, G.14, M.15, G.16, K.17, T.18, R.171 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.14, A:M.15, A:G.16, A:K.17, A:T.18, A:R.171 Water bridges: A:T.18 Salt bridges: A:K.17 SO4.3: 3 residues within 4Å: Chain A: K.272, R.275, S.276 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.276, A:S.276 Salt bridges: A:K.272, A:R.275 SO4.5: 6 residues within 4Å: Chain B: H.13, G.14, M.15, G.16, R.175, R.177 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.14, B:M.15, B:G.16 Salt bridges: B:R.175, B:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pernot, L. et al., New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer. To be Published

Release Date

2013-02-06

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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